I think that jat is right - if you have a builder defined on your project that Eclipse does not know about, it will throw an exception.
For now, let's go with this update to the README. I think, as a future step, we should add the natures and builders to the gwt-user and gwt-dev project, and make it a necessary step for them to install GPE. http://gwt-code-reviews.appspot.com/966802/show -- http://groups.google.com/group/Google-Web-Toolkit-Contributors
